7WUO

Unravelling structure of riboflavin synthase for designing of potential anti-bacterial drug

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	288.15	0.2 M Ammonium Sulfate, 0.1M MES monohydrate (pH 6.5), 10% w/v PEG MME 5000

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.559	α = 90
b = 130.632	β = 90
c = 202.5	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	RIGAKU	dextris 200k	2019-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3.19	40	97.4	0.163	9.2	4.4		13224

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.26	99.9		0.464	0.818	2.9	4.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1I8D	3.19	27.26	12554	636	97.23	0.2204	0.2182	0.2638	RANDOM	39.875

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.31			-2.54		2.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.415
r_dihedral_angle_4_deg	18.836
r_dihedral_angle_3_deg	18.418
r_dihedral_angle_1_deg	8.193
r_angle_refined_deg	1.615
r_angle_other_deg	1.251
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.415
r_dihedral_angle_4_deg	18.836
r_dihedral_angle_3_deg	18.418
r_dihedral_angle_1_deg	8.193
r_angle_refined_deg	1.615
r_angle_other_deg	1.251
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4604
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	14

Software

Software
Software Name	Purpose
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.